Sample Publications

  1. Weirick I, Uchida S.  (2018) Maximizing the information extraction of RNA-seq data for achieving personalized medicineHuman Genomics, 12.
  2. Uchida S, Jones SP.  (2018) RNA Editing: Unexplored opportunities in the cardiovascular systemCirculation Research, 122(3):399-401.
  3. Weirick T, Militello G, Uchida S.  (2018) Long non-coding RNAs in endothelial biology.  Frontiers in Physiology 9:522.
  4. Zahin M, Dean WL, Ghim S, Joh J, Gray RD, Khanal S, Bossart GD, Mignucci-Giannoni AA, Rouchka EC, Jenson AB, Trent JO, Chaires JB, Chariker JH.  (2018) Identification of G-quadruplex forming sequences in three manatee papillomavirusesPLoS One 13(4):e0195625.
  5. Merchant ML, Brier ME, Slaughter MS, Klein JB, McLeish KR.  (2018) Biomarker enhanced risk prediction for development of AKI after cardiac surgery BMC Nephrology 19(1):102.
  6. Kalbfleisch TS, Murdoch BM, Smith TPL, Murdoch JD, Heaton MP, McKay SD. (2018) A SNP resource for studying North American moose.  F1000Research 7:40.
  7. Schultz DJ, Krishna A, Vittitow SL, Alizadeh-Rad N, Muluhngwi P, Rouchka EC, Klinge CM.  (2018) Transcriptomic response of breast cancer cells to anacardic acid.  Scientific Reports.
  8. Heathon MP, Smith TPL, Freking BA, Workman AM, Bennet GL, Carnahan JK, Kalbfleisch TS. (2017) Using sheep genomes from diverse US breeds to identify missense variants in genes affecting fecundityF1000Research 6:1303.
  9. Schultz DJ, Muluhngwi P, Alizadaeh-Rad N, Rouchka EC, Klinge, CM.  (2017) Genome-wide miRNA response to anacardic acid in breast cancer cells.  PLoS One 12(9):e0184471.
  10. Toh SS, Chen Z, Rouchka EC, Schultz DJ, Cuomo CA, Perlin MH.  (2017) Pas de deux: An intricate dance of anther smut and its host. G3: Genes, Genomes, Genetics.
  11. Merchant ML, Rood IM, Deegens JKJ, Klein JB.  (2017) Isolation and characterization of urinary extracellular vesicles: implications for biomarker discovery Nature Reviews Nephrology, 13(12):731-749.
  12. Uchida S, Bolli R.  (2017) Short and long noncoding RNAs regulate the epigenetic status of cells.  Antioxidants and Redox Signaling.
  13. Uchida S.  (2017) High-throughput methods to detect long non-coding RNAs. High-Throughput, 6(3):12.
  14. Saka E, Harrison BJ, West K, Petruska JC, Rouchka EC.  (2017) Framework for reanalysis of publicly available Affymetrix® GeneChip® data sets based on functional regions of interest. BMC Genomics 18(Suppl 10):875.
  15. Smelter A*, Rouchka EC, Moseley H. (2017) Detecting and accounting for multiple sources of positional variance in peak list registration and spin system grouping.  Journal of Biomolecular NMR, 68(4):281-296.
  16. Li X, Brock GN, Rouchka EC, Cooper NGF, Wu D, O’Toole T, Gill RS, Eteleeb AM, O’Brien L, Rai SN.  (2017) A comparison of per sample global scaling and per gene normalization methods for differential expression analysis of RNA-seq data.  PLoS One 12(5):e0176185.
  17. DeFilippis AP, Trainor PJ*, Hill BG, Amraotkar AR, Rai SN, Hirsch GA, Rouchka EC, Bhatnagar A. (2017) Identification of a plasma metabolomic signature of thrombotic myocardial infarction that is distinct from non-thrombotic myocardial infarction and stable coronary artery disease.  PLoS One. 12(4):e0175591.
  18. Trainor P*, Hill BG, Carlisle SM, Rouchka EC, Rai SN, Bhatnagar A, DeFilippis AP.  (2017) Systems characterization of differential plasma metabolome perturbations following thrombic and non-thrombic myocardial infarctionJournal of Proteomics. S1874-3919(17):30098-2.
  19. Yao S*, Flight RM, Rouchka EC, Moseley HNB.  (2017) Aberrant coordination geometries discovered in the most abundant metalloproteins. Proteins: Structure, Function, and Bioinformatics. 85(5):885-907.
  20. Li X, Cooper NGF, Shyr Y, Wu D, Rouchka EC, Gill RS, O’Toole TE, Brock GN, Rai SN.  (2017) Inference and sample size calculations based on statistical tests in a negative binomial distribution for differential gene expression in RNA-seq experimental designJournal of Biometrics and Biostatistics 8:332.
  21. Soliman M, Andreeva K, Nasraoui O, Cooper NGF. (2017) A causal mediation model of ischemia reperfusion injury in the retina.PLoS One. 12(11):e0187426.
  22. Chaabane M, Rouchka EC, Park JW.  Circular RNA Detection from High-throughput SequencingProceedings of the International Conference on Research in Adaptive and Convergent Systems (RACS 2017), pp. 19-24. September 20-23, 2017, Krakow, Poland.
  23. Lin L, Jiang P, Park JW, Wang J, Lu Z, Lam MPY, Ping P, Xing Y. (2016) The contribution of Alu exons to the human proteomeGenome Biology 17(1):15.
  24. Chariker JL, Miller DM, Rouchka EC. (2016) Computational analysis of G-quadruplex forming sequences across chromosomes reveals high density patterns near the terminal endsPLoS One 11(10): e0165101.
  25. Park JW, Jung S, Rouchka EC, Tseng T, Xing Y.  (2016) rMAPS: RNA Map Analysis and Plotting Server for Alternative Exon RegulationNucleic Acids Research. 44(W1):W333-338.
  26. Soliman M, Nasraoui O, Cooper NG.  (2016) Building a glaucoma interaction network using a text mining approachBioData Mining 9:17.
  27. Weirick T, Militello G, Ponomareva Y, John D, Doring C, Dimmeler S, Uchida S.  (2016) Logic programming to infer complex RNA expression patterns from RNA-seq dataBriefings in bioinformatics, bbw117.
  28. John D, Weirick T, Dimmeler S, Uchida S.  (2016) RNAEditor: easy detecton of RNA editing events and the introduction of editing islandsBriefings in bioinformatics, 18(6):993-1001.
  29. Muller R, Weirick T, John D, Militello G, Chen W, Dimmeler S, Uchida S. (2016) ANGIOGENES: knowledge database for protein-coding and noncoding RNA genes in endothelial cellsScientific Reports, 6:32475.
  30. Militello G, Weirick T, John D, Doring C, Dimmeler S, Uchida S.  (2016) Screening and validation of lncRNAs and circRNAs as miRNA spongesBriefings in Bioinformatics, bbw053.
  31. Weirick T, John D, Uchida S.  (2016) Resolving the problem of multiple accessions of the same transcript deposited across various public databasesBriefings in Bioinformatics 18(2):226-235.
  32. Heaton MP, Smith TP, Carnahan JK, Basnayake V, Qiu J, Simpson B, Kalbfleisch TS.  (2016) Using diverse US beef cattle genomes to identify missense mutations in EPAS1, a gene associated with pulmonary hypertensionF1000Research 5:2003.
  33. Rebolledo-Mendez J, Hestand MS, Coleman SJ, Zeng Z, Orlando L, MacLeod JN, Kalbfleisch T.  (2015) Comparison of the equine reference sequence with its Sanger source data and new Illumina readsPLoS One 10(6):e0126852.
  34. Weirick T, Militello G, Muller R, John D, Dimmeler S, Uchida S.  (2015) The identification and characterization of novel transcripts from RNA-seq dataBriefings in Bioinformatics, 17(4):678-685.
  35. Weirick T, John D, Dimmeler S, Uchida S.  (2015) C-It-Loci: a knowledge database for tissue-enriched lociBioinformatics, 31(21):3537-3543.
  36. Yao S*, Flight RM, Rouchka EC, Moseley HNB.  (2015) A less biased analysis of metalloproteins reveals novel zinc coordination geometriesProteins: Structure, Function, and Bioinformatics. 83(8):1470-1487.
  37. Andreeva K, Soliman MM, Cooper NG.  (2015) Regulatory networks in retinal ischemia-reperfusion injury.  BMC Genetics 16:43.
  38. Mattingly WA, Chariker JH, Paris R, Chang D-J, Pani JR. (2015). 3D Modeling of Branching Structures for Anatomical Instruction. Journal of Visual Languages and Computing, 29, 54-62.
  39. Gill R, Datta S, Datta S. (2014) dna: An R package for differential network analysisBioinformation 10(4):233-234.
  40. Shen S, Park JW, Lu Z, Lin L, Henry MD, Wu YN, Zhou Q, Xing Y.  (2014) rMATS: robust and flexible detection of differential alternative splicing from replicate RNA-Seq dataProceedings of the National Academy of Sciences, 111(51):E5593-E5601.
  41. Tokheim C, Park JW, Xing Y.  (2014) PrimerSeq: design and visualization of RT-PCR primers for alternative splicing using RNA-seq data.  Genomics, proteomics & bioinformatics, 12(2):105-109.
  42. Eteleeb AM, Moseley HN, Rouchka EC. (2014) A Comparison of Combined P-value Methods for Gene Differential Expression Using RNA-Seq Data.  Proceedings of the Fifth International Conference on Bioinformatics, Computational Biology and Biomedical Informatics (ACM-BCB 2014), pp. 417-425. September 20-23, 2014, Newport Beach, CA.
  43. Harrison BJ, Flight RM, Gomes C, Venkat G, Ellis SR, Sankar U, Twiss JL, Rouchka EC, Petruska JC.  (2014) IB4-binding sensory neurons in the adult rat express a novel 3’ UTR-extended isoform of CAMK4 that is associated with its localization to axons.  The Journal of Comparative Neurology, 522(2):308-336.
  44. Flight RM, Harrison BJ, Mohammad F, Bunge MB, Moon LDF, Petruska JC, Rouchka EC.  (2014) categoryCompare, an analytical tool based on feature annotationsFrontiers in Genetics, 5:98.
  45. Schubert M, Jónsson H, Chang D, Der Sarkissian C, Ermini L, Ginolhac A, Albrechtsen A, Dupanloup I, Foucal A, Petersen B, Fumagalli M, Raghavan M, Seguin-Orlando A, Korneliussen TS, Velazquez AM, Stenderup J, Hoover CA, Rubin CJ, Alfarhan AH, Alquraishi SA, Al-Rasheid KA, MacHugh DE, Kalbfleisch T, MacLeod JN, Rubin EM, Sicheritz-Ponten T, Andersson L, Hofreiter M, Marques-Bonet T, Gilbert MT, Nielsen R, Excoffier L, Willerslev E, Shapiro B, Orlando L.  (2014) Prehistoric genomes reveal the genetic foundation and cost of horse domestication. Proc Natl Acad Sci U S A.  111(52):E5661-E5669.
  46. Heaton MP, Leymaster KA, Kalbfleisch TS, Kijas JW, Clarke SM, McEwan J, Maddox JF, Basnayake V, Petrik DT, Simpson B, Smith TP, Chitko-McKown CG; International Sheep Genomics Consortium. (2014) SNPs for parentage testing and traceability in globally diverse breeds of sheep.  PLoS One, 9(4):e94851. 
  47. Andreeva K, Zhang M, Fan W, Li X, Chen Y, Rebolledo-Mendez JD, Cooper NG. (2014) Time-dependent Gene Profiling Indicates the Presence of Different Phases for Ischemia/Reperfusion Injury in Retina. Ophthalmol Eye Dis. 6:43-54.
  48. Andreeva K, Cooper NG.  (2014) MicroRNAs in the Neural RetinaInt J Genomics 2014: 165897.
  49. Naaz F, Chariker JH, Pani JR.  (2014) Computer-based learning: Graphical integration of whole and sectional neuroanatomy improves long-term retentionCogn Instr 32(1):44-64.
  50. Pani JR, Chariker JH, Naaz F, Mattingly W, Roberts J, Sephton SE. (2014) Learning with interactive computer graphics in the undergraduate neuroscience classroomAdv Health Sci Educ Theory Pract 19(4):507-28.
  51. Mohammad F, Flight RM, Harrison BJ, Petruska JC, Rouchka EC.  (2012) AbsIDconvert: An Absolute Approach for Converting Genetic Identifiers at Different Granularities.  BMC Bioinformatics 2012, 13:229.
  52. Heaton MP, Kalbfleisch TS, Petrik DT, Simpson B, Kijas JW, Clawson ML, Chitko-McKown CG, Harhay GP, Leymaster KA, International Sheep Genomics Consortium. (2013) Genetic testing for TMEM154 mutations associated with lentivirus susceptibility in sheep. PLoS One, 8(2):e55490.
  53. Rebolledo-Mendez JD, Vaishnav RA, Cooper NG, Friedland RP. (2013) Cross-kingdom sequence similarities between human micro-RNAs and plant viruses. Commun Integr Biol 6(5): e24951. 
  54. Zhao K, Lu Z, Park JW, Zhou Q, Xing Y.  (2013) GLiMMPS: robust statistical model for regulatory variation of alternative splicing using RNA-seq data.  Genome Biology 14(7):R74.
  55. Park JW, Tokheim C, Shen S, Xing Y.  (2013) Identifying differential alternative splicing events from RNA sequencing data using RNASeq-MATS.  Deep Sequencing Data Analysis, 171-179.